User-level MCP setup (no wrapper)

March 9, 2026 · View on GitHub

How to run MCP servers (e.g. GitHub) from your user config using a shared .env in %USERPROFILE%\.env\ (e.g. C:\Users\<you>\.env\ on Windows). No wrapper script.

1. User-level config location

  • Windows: %USERPROFILE%\.cursor\mcp.json (e.g. C:\Users\<you>\.cursor\mcp.json).
  • This applies to all workspaces. Workspace .cursor/mcp.json is separate and can coexist.

2. GitHub MCP without wrapper

Use command + args + env; do not use python .cursor/mcp_wrapper.py ....

Example user mcp.json (only the servers you want at user level):

{
  "mcpServers": {
    "user-github": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "<paste from your .env file>"
      }
    }
  }
}

Replace <paste from .env...> with your token. Manually copy values from your .env file into the env object.

3. Shared .env in %USERPROFILE%\.env\

Cursor does not load .env files automatically. To use a single file for secrets:

  1. Create the directory: %USERPROFILE%\.env\ (e.g. C:\Users\<you>\.env\)
  2. Copy the repo’s .env.example there as .env: %USERPROFILE%\.env\.env
  3. Edit %USERPROFILE%\.env\.env and set at least:
    • GITHUB_PERSONAL_ACCESS_TOKEN=<your-token>
  4. Put those same values into the env object of your user mcp.json (see §2).

So: user-level .cursor “uses” the file by you copying values from %USERPROFILE%\.env\.env into mcp.json’s env. Cursor does not read that path by itself.

4. Restart

After editing user mcp.json, fully restart Cursor (quit the app, then open again) so the MCP client picks up the new config.